Making model and animation for Unity using MakeHuman and Blender
MakeHuman ships with the "Game Engine Rig", which is compatible with the mecanim unity functionality. The appropriate work flow is:


Enable the game engine rig in makehuman (under pose -> skeleton)
Export using mhx2
In blender, either import without overrides or make sure to leave the rig as it is upon import


You only get the MHX rig if you explicitly ask for it when importing an MHX file in blender. Otherwise, the rig exported from MakeHuman will be used. 

As an alternative to using MHX2, there is also a new pipeline for integrating MakeHuman and blender, see https://www.youtube.com/watch?v=tAwfR-G813g